Building

Testing software

First test that software is correctly installed, you must first follow this tutorial:

https://github.com/opencb/cellbase/wiki/installation

Go to CellBase folder and:

cd cellbase/cellbase-build/installation-dir

cellbase-build/installation-dir

You must get something like:

usage: cellbase-build.jar --build [--cosmic-file <arg>]
   [--description-file <arg>] [--fasta-file <arg>] [--gtf-file <arg>]
   [-i <arg>] [--log-level <arg>] [--mirna-file <arg>] -o <arg>
   [--psimi-tab-file <arg>] [-s <arg>] [--tfbs-file <arg>]
   [--xref-file <arg>]
Some options are mandatory for all possible 'builds', while others are
only mandatory for some specific 'builds':
--build                    Build values: core, genome_sequence,
                           variation, protein
--cosmic-file <arg>        Output directory to save the JSON result
--description-file <arg>   Output directory to save the JSON result
--fasta-file <arg>         Output directory to save the JSON result
--gtf-file <arg>           Output directory to save the JSON result

-i,--indir Input directory with data files --log-level DEBUG -1, INFO -2, WARNING - 3, ERROR - 4, FATAL - 5 --mirna-file Output directory to save the JSON result -o,--output Output file or directory (depending on the 'build') to save the result --psimi-tab-file Output directory to save the JSON result -s,--species Sapecies... --tfbs-file Output directory to save the JSON result --xref-file Output directory to save the JSON result For more information or reporting bugs contact me: [email protected]